Research workbench
Structure of electron bifurcating ni-fe hydrogenase complex hydabcsl in FMN/NAD(H) bound state
Analyse Structure of electron bifurcating ni-fe hydrogenase complex hydabcsl in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T30
- Type
- protein
- Length
- 3,578 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nife hydrogenase subunit a; Nife hydrogenase subunit B; Nife hydrogenase subunit C; Nife…
- UniProt
- I4BYB4, I4BYB5, I4BYB8, I4BYB2, I4BYB3
- Ligands
- SF4, FES, NAD, FMN, FCO, 3NI
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 5 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Nife hydrogenase subunit a | protein | 666 | 30% helix, 13% strand | I4BYB4 |
| B, G | Nife hydrogenase subunit B | protein | 425 | 42% helix, 12% strand | I4BYB5 |
| C, H | Nife hydrogenase subunit C | protein | 72 | 60% helix, 0% strand | I4BYB8 |
| D, I | Nife hydrogenase large subunit | protein | 447 | 44% helix, 17% strand | I4BYB2 |
| E, J | Nife hydrogenase small subunit | protein | 179 | 33% helix, 16% strand | I4BYB3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains A, B, D, E, F, G, I, J
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B, F, G
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, G
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, G
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains D, I
- 3NI · Nickel (III) ion · metal · 2 copies · chains D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.77 | 0.81 | 69 | NAD, FMN |
| 2 | 801 | 0.77 | 0.81 | 69 | NAD, FMN |
| 3 | 785 | 0.73 | 0.78 | 64 | empty |
| 4 | 789 | 0.73 | 0.78 | 58 | empty |
| 5 | 53 | 0.72 | 0.99 | 20 | empty |
Interfaces
14 interfaces between chains.
- I–J · 2763 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2746 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1489 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1482 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1040 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7T30 · Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN/NAD(H) bound… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt I4BYB4
- Every structure of UniProt I4BYB5
- Every structure of UniProt I4BYB8
- Every structure of UniProt I4BYB2
- Every structure of UniProt I4BYB3
- Elsewhere: RCSB PDB 7T30 · PDBe 7T30 · UniProt I4BYB4 · UniProt I4BYB5 · UniProt I4BYB8 · UniProt I4BYB2 · UniProt I4BYB3
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